RStudio Conference 2022

• Quarto Publishing System: https://quarto.org
• Mine and Julia’s talk about Collaborating with Quarto
• Joe Cheng’s Shiny Talk

What is Quarto?

• Reproducible Publishing System based on Pandoc
• One format, many outputs
  • Website
  • Publications
  • Books
  • Dashboards

.qmd files

• Short for quarto markdown
• Decoupled from RStudio IDE
  • plugins for VSCode, JupyterLab and RStudio are available
• Can still Render within RStudio
• Render with quarto standalone on command line:

quarto render my_document.qmd

Cross Language Support

• Supports a number of languages:
  • R
  • Python
  • Julia
  • Observable
• Can interchange between langugages using Apache Arrow

Jupyter Notebook Support

• Jupyter Notebooks are cross compatible
• One command to interchange:

quarto convert notebook.ipynb

Fast way to publish Jupyter Notebooks!

Code Output Freezing

• By default, code is not recomputed
• quarto render --execute will recompute
• Output is “frozen”

execute:
  freeze: auto  # re-render only when source changes

Code Chunks

Options are moved to within the code chunk using #| (hash-pipe) for each line

RMarkdown

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```

Quarto

```{r}
#| label = "setup",
#| include = FALSE
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```

How is Quarto different from RMarkdown?

• Standardized YAML across formats
• Decoupled from RStudio
• More consistent presentation across formats
• Tab Panels
• Code Highlighting

Should I Switch to Quarto?

Should you switch to Quarto? Not necessarily. If you find R Markdown meet your need, you can definitely stay there. It is not imperative to switch. Quarto’s goal is to cover most features of R Markdown eventually, but it may be impossible to become a strict superset of R Markdown. - Yihui Xie

Some Killer Apps for Quarto (HTML)

• Precise Layouts
• Tab Panels
• Code Highlighting

Layout Example

:::: {.columns}

::: {.column width="50%"}
- Highly customizable
- Less work than using `<div>` tags
:::

::: {.column width="50%"}
- Customizable in terms of layouts

:::
::::

Layout Example

Tabsets

::: {.panel-tabset}

### Code

This is where I would put some code:

### Figure

:::

Tabsets

```{r}
library(palmerpenguins)
library(ggplot2)
data(penguins)
ggplot(penguins, aes(x=bill_depth_mm, y=bill_length_mm, color = species)) + geom_point()
```

Code Highlighting

• Incremental highlighting (line by line)
• Killer app for me
• Really good for teaching!

```{r}
#| echo: TRUE
#| eval: FALSE
#| code-line-numbers: "3|4-6|7"
library(palmerpenguins)
library(ggplot2)
data(penguins)
ggplot(penguins) + aes(x=bill_depth_mm, 
                       y=bill_length_mm, 
                       color = species) + 
  geom_point()
```

Code Highlighting Example

library(palmerpenguins)
library(ggplot2)
data(penguins)
ggplot(penguins) + aes(x=bill_depth_mm, 
                       y=bill_length_mm, 
                       color = species) + 
  geom_point()

Checklist

1. Start a Quarto Project
2. For your documents: Change your output: to the corresponding format: in your YAML
3. Use knitr::convert_chunk_header() to convert your code blocks (outputs a .qmd file)
4. Render your files
5. For websites: edit your _quarto.yml file if necessary

1. Start a Quarto Project

2. Convert your Rmarkdown Documents

• Change your YAML header
• Instead of output:, use format:

2. RMarkdown/Quarto Formats

3. Convert your RMarkdown Code Chunks

knitr::convert_chunk_header() will convert your RMarkdown code chunks into quarto compatible format.

knitr::convert_chunk_header("filename.Rmd", 
    output = "filename.qmd")

3. Converting Code Chunks

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```

```{r}
#| label = "setup",
#| include = FALSE
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(DT)
library(ggimage)
```

4. Render via RStudio GUI

• Render button in RStudio

quarto::quarto_render()`

4. Render via Command Line

> quarto render <filename>

5. Update your _quarto.yml for websites

• Controls navigation and visibility of documents

project:
  type: website

website:
  title: "Ted Laderas, PhD"
  description: "Ted's R and Teaching Blog"
  navbar:
    right:
      - teaching.qmd
      - articles.qmd
      - blog.qmd
      - talks.qmd

Publish your files (on CLI)

quarto publish can push and update a number of different kinds of webhosts.

quarto publish gh-pages    # GitHub Pages
quarto publish quarto-pub  # Quarto.pub 
quarto publish netlify     # Netlify
quarto publish connect     # RStudio Connect

Conclusions

• Quarto supports multiple languages / IDEs
• Quarto standardizes a lot of outputs
• Does a better job of one document, many outputs
• Lots of publishing features (references, figures, etc.)

Learn More

Workshop materials from Andrew Bray: https://github.com/rstudio-conf-2022/rmd-to-quarto

Observable + Shiny + Quarto

• Rapid prototyping of responsive dashboards
• Uses Observable for front end
• Uses Shiny reactives for backend
• Quarto for Layout